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Handbook of Research on Computational Grid Technologies for Life Sciences, Biomedicine, and Healthcare (2009) 121-148 p.
High Performance Blast over the Grid
V. Breton1, Eddy Caron2, Frédéric Desprez2, Gaël Le Mahec1

As grids become more and more attractive for solving complex problems with high computational and storage requirements, bioinformatics algorithms start to be ported on large scale platforms. The BLAST kernel was one the first application ported on such platform. However, although simple parallelization was enough for the first proof of concept, its use in production platform needed more optimized algorithms. The chapter reviews existing parallelization and “gridification” of the BLAST algorithm as well as related issues such as data management and replication. A case study using the DIET middleware over the Grid'5000 experimental platform is also presented.
1 :  LPC - Laboratoire de Physique Corpusculaire [Clermont-Ferrand]
2 :  INRIA Grenoble Rhône-Alpes / LIP Laboratoire de l'Informatique du Parallélisme - GRAAL

Sciences du Vivant/Bio-Informatique, Biologie Systémique

Informatique/Calcul parallèle, distribué et partagé